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Last updated on 2025-03-09

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Yan Shi HU (胡言石)

Being at the forefront of interdisciplinary research is incredibly exciting. It opens up new avenues for pushing the boundaries of our wisdom. My main interests lie in leveraging AI, bioinformatics and computational (systems) biology to advance insights into major complex diseases. Currently I am deeply fascinated by decyphering large-scale disease comorbidity patterns and detailed disease comorbidity between Parkinson's and Crohn's disease.

I have authored 12 SCI papers, which have been widely cited by academic articles published in high-impact journals such as Science, Gastroenterology, Pharmacological Reviews, Trends in Neurosciences, Trends in Cancer, Alzheimer's & Dementia, Trends in Genetics, Brain and Nucleic Acids Research. Currently I serve as (ad hoc) peer reviewer for 17 SCI journals.

Research Interests:
AI4BioMed | NetBioMed | Computational (Systems) Biology | Neuroscience

WORKING EXPERIENCE

Research Associate

College of Life Sciences
Zhejiang University

Hangzhou, China

2025 - 2023

Research Assistant

School of Biomedical Engineering
Tianjin Medical University

Tianjin, China

2017 - 2016

EDUCATION

Doctor of Philosophy in Bioinformatics

Zhejiang University

Hangzhou, China

  • Dissertation: Systems biology analyses of molecular mechanisms underlying comorbidity between Parkinson's and Crohn's disease
  • Adviser: Prof. Ming Chen (陈铭)

2023 - 2017

Master of Philosophy in Biomedical Engineering

Tianjin Medical University

Tianjin, China

2016 - 2013

  • Dissertation: Biochemical pathway and protein-protein interaction network based analyses of genes associated with Parkinson's disease
  • Adviser: Prof. Ju Wang (王举)

Bachelor of Science in Biomedical Engineering

Shandong First Medical University
Shandong Academy of Medical Sciences

Taian, China

2013 - 2009

  • Dissertation: Comparative study of three MATLAB based methods for retinal image brightness and contrast adjustment
  • Adviser: Prof. Yongxin Guo (郭永新)

ACADEMIC HONORS & AWARDS

Bioinformatics Society of Zhejiang Province of China, Membership

Bioinformatics Society of Zhejiang Province of China

N/A

2025 - 2017

Zhejiang University Award of Honor for Graduate

Zhejiang University

N/A

2019

Zhejiang University First-Class Scholarship for Doctoral Mid-term Examination

Zhejiang University
Scholarship amount: ¥ 20,000

N/A

2018

Zhejiang University Award of Honor for Graduate

Zhejiang University

N/A

Zhejiang University Excellent Doctoral Freshman Scholarship

Zhejiang University
Scholarship amount: ¥ 10,000

N/A

2017

Second-Class Prize for Excellent Poster

The 6th National Conference on Bioinformatics & Systems Biology of China (第六届全国生物信息学与系统生物学学术大会)
Prize amount: ¥ 400

N/A

2014

Shandong First Medical University Excellent Undergraduate Thesis Award

Shandong First Medical University
Shandong Academy of Medical Sciences

N/A

2013

Shandong First Medical University Second-Class Scholarship

Shandong First Medical University
Shandong Academy of Medical Sciences

N/A

2011

Shandong First Medical University Third-Class Scholarship

Shandong First Medical University
Shandong Academy of Medical Sciences

N/A

2010


SCI JOURNAL REFEREE

Science China-Life Sciences

Impact Factor: 8.0

N/A

# 1

Bioinformatics

Impact Factor: 7.6

N/A

# 2

International Journal of Intelligent Systems

Impact Factor: 5.9

N/A

# 3

Molecular Neurobiology

Impact Factor: 5.1

N/A

# 4

Frontiers in Neuroscience

Impact Factor: 4.3

N/A

# 5

Scientific Reports

Impact Factor: 4.3

N/A

# 6

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Impact Factor: 3.6

N/A

# 7

Frontiers in Neurology

Impact Factor: 3.3

N/A

# 8

PLOS ONE

Impact Factor: 3.3

N/A

# 9

Journal of Molecular Neuroscience

Impact Factor: 2.8

N/A

# 10

Mammalian Genome

Impact Factor: 2.7

N/A

# 11

Computational Biology and Chemistry

Impact Factor: 2.6

N/A

# 12

BMC Medical Genomics

Impact Factor: 2.5

N/A

# 13

BMC Neurology

Impact Factor: 2.5

N/A

# 14

Current Bioinformatics

Impact Factor: 2.4

N/A

# 15

Cell Biochemistry and Biophysics

Impact Factor: 2.0

N/A

# 16

BMC Genomic Data

Impact Factor: 1.9

N/A

# 17





PUBLICATIONS & PREPRINTS

Decrypting human biological pathway crosstalk landscape in a deep learning architecture

To Appear on bioRχiv.

N/A

2025

YS Hu#, Y Chen#, Y Hu, M Chen*

AWmeta empowers adaptively-weighted meta-analysis for gene expression data

To Appear on bioRχiv.

N/A

N/A

YS Hu, Z Wang, Y Hu, M Chen*

HPInet: Interpretable prediction of Host-Pathogen protein–protein Interactions using a transformer-based neural network

Under Review, Briefings in Bioinformatics.

Impact Factor:7.9

N/A

YM Hu#, LY Liu#, YY Zhu#, EY Liu, HY Chao, SD Li, C Feng, YS Hu, YH Chen, S Zhang, Y Chen, L Xie, Y Wang, M Chen*

Improved Prediction of Bacterial Type VI Secretion Effector Proteins Using an Integrated Convolutional Neural Network Model Combining N-terminal Signal Sequences, Evolutionary Information and Pre-Trained Protein Language Features

Under Review, mSystems.

Impact Factor:6.1

N/A

YM Hu#, MQ Yan#, Y Zhu, H Chao, S Li, Q Ni, YS Hu, EY Liu, LY Liu, Y Chen, Z Zhou, Y Chen, S Zhang, Y Wang, C Feng*, M Chen*

Benchmarking alternative polyadenylation detection in single-cell and spatial transcriptomes

bioRχiv. 2024.10.15.618405. (Under Review, Genome Biology)

N/A

2024

S Li, Z Wang, YS Hu, Q Ni, C Feng, Y Hu, S Zhang, M Chen*

ncPlantDB: a plant ncRNA database with potential ncPEP information and cell type-specific interaction

Nucleic Acids Research. 2024, gkae1017.

Impact Factor: 16.6

N/A

L Liu#, E Liu#, Y Hu, S Li, S Zhang, H Chao, YS Hu, Y Zhu, Y Chen, L Xie, Y Shen, L Wu, M Chen*

Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition

BMC Biology. 2024, 22(1):143.

Impact Factor: 5.4

N/A

C Feng#, RX Tie#, SG Xin#, YH Chen, SD Li, YF Chen, XT Hu, YC Zhou, YJ Liu, YM Hu, YS Hu, H Pan, ZX Wu, HY Chao, SL Zhang, QY Ni, J Huang, W Luo*, H Huang*, M Chen*

HALD, a human aging and longevity knowledge graph for precision gerontology and geroscience analyses

Scientific Data. 2023, 10(1):851.

Impact Factor: 8.9

2023

Z Wu#, C Feng#, YS Hu, Y Zhou, S Li, S Zhang, Y Hu, Y Chen, H Chao, Q Ni, M Chen*

CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure

Bioinformatics. 2022, 38(18):4380-4386.

Impact Factor: 7.6

2022

Y Chen#, YS Hu#, X Hu, C Feng, M Chen*

CoVM2: Molecular Biological Data Integration of SARS-CoV-2 Proteins in a Macro-to-Micro Method

Biomolecules. 2022, 12(8):1067.

Impact Factor: 5.4

N/A

H Chen, X Hu, YS Hu, J Zhou, M Chen*

LBD: a manually curated database of experimentally validated lymphoma biomarkers

Database. 2022, Volume 2022, baac051.

Impact Factor: 4.2

N/A

B Tan, S Xin, YS Hu, C Feng*, M Chen*

PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants

Database. 2020, Volume 2020, baaa001.

Impact Factor: 4.2

2020

W Wu, Y Wu, D Hu, Y Zhou, YS Hu, Y Chen, M Chen*

The inflammatory cytokine IL-6 induces FRA1 deacetylation promoting colorectal cancer stemness and malignancy

Oncogene. 2019, 38:4932-4947.

Impact Factor: 7.5

2019

T Wang, P Song, T Zhong, X Wang, X Xiang, Q Liu, H Chen, T Xia, H Liu, Y Niu, YS Hu, L Xu, Y Shao, L Zhu, H Qi, J Shen, T Hou, R Fodde*, J Shao*

Network and Pathway-Based Analyses of Genes Associated with Parkinson’s Disease

Molecular Neurobiology. 2017, 54(6):4452-4465.

Impact Factor: 5.1

N/A

YS Hu, Z Pan, Y Hu, L Zhang*, J Wang*

Detecting pathway relationship in the context of human protein-protein interaction network and its application to Parkinson’s disease

Methods. 2017, 131:93-103.

Impact Factor: 4.2

N/A

Y Hu, Y Yang, Z Fang, YS Hu, L Zhang*, J Wang*

GRONS: a comprehensive genetic resource of nicotine and smoking

Database. 2017, Volume 2017, bax097.

Impact Factor: 4.2

N/A

Z Fang, Y Yang, YS Hu, MD Li*, J Wang*

CONFERENCE PROCEEDINGS

Network and pathway based analyses of genes associated with Parkinson’s disease

The 7th National Conference on Bioinformatics and Systems Biology of China

Chengdu, China

2016

Uncovering the common pathogenesis in neurodegenerative and psychiatric disorder via network approaches

The 7th National Conference on Bioinformatics and Systems Biology of China

Chengdu, China

N/A

Common characteristics of Alzheimer’s disease and Parkinson’s disease based on AlzGene and PDGene databases

The 6th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

2014

Computing the phenotype similarity based on OMIM database and MESH vocabulary

The 6th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

N/A

TarPriGO: a new method to prioritize miRNA targets based on Gene Ontology

The 6th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

N/A

A comprehensive pathway and network analysis of candidate genes associated with nicotine addiction

The 6th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

N/A

The functional divergence analysis of neuronal nicotinic acetylcholine receptor subunits

The 6th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

N/A

ACADEMIC TALKS

Zhejiang University-Bielefeld University Joint Symposium

Talk Title: Analyzing the genes related to Alzheimer’s disease via a network and pathway-based approach

Bielefeld, Germany

2019

First Sino-Russian Workshop on Integrative Bioinformatics and Systems Biology (WIBSB-2018)

Talk Title: Analyzing the genes related to Alzheimer’s disease via a network and pathway-based approach

Novosibirsk, Russia

2018

ACADEMIC POSTERS

Network and pathway based analyses of genes associated with Parkinson’s disease

The 7th National Conference on Bioinformatics and Systems Biology of China

Chengdu, China

2016

Common characteristics of Alzheimer’s disease and Parkinson’s disease based on AlzGene and PDGene databases

The 6th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

2014

PATENTS

一种生化通路串话识别方法 (Chinese Patent)

Inventor: 陈铭,胡言石 (Yan Shi HU),陈俞皓

Application Number: 2023107816823
Filing Date: 2023-06-28
Publication number: CN116959588A
Publication Date: 2023-10-27

N/A

2023